Cell reports, 2019
Authors
Chun, Hye-Jung E, Johann, Pascal D, Milne, Katy, Zapatka, Marc, Buellesbach, Annette, Ishaque, Naveed, Iskar, Murat, Erkek, Serap, Wei, Lisa, Tessier-Cloutier, Basile, Lever, Jake, Titmuss, Emma, Topham, James T, Bowlby, Reanne, Chuah, Eric, Mungall, Karen L, Ma, Yussanne, Mungall, Andrew J, Moore, Richard A, Taylor, Michael D, Gerhard, Daniela S, Jones, Steven J M, Korshunov, Andrey, Gessler, Manfred, Kerl, Kornelius, Hasselblatt, Martin, Frühwald, Michael C, Perlman, Elizabeth J, Nelson, Brad H, Pfister, Stefan M, Marra, Marco A, Kool, Marcel
Publication Abstract
Extra-cranial malignant rhabdoid tumors (MRTs) and cranial atypical teratoid RTs (ATRTs) are heterogeneous pediatric cancers driven primarily by SMARCB1 loss. To understand the genome-wide molecular relationships between MRTs and ATRTs, we analyze multi-omics data from 140 MRTs and 161 ATRTs. We detect similarities between the MYC subgroup of ATRTs (ATRT-MYC) and extra-cranial MRTs, including global DNA hypomethylation and overexpression of HOX genes and genes involved in mesenchymal development, distinguishing them from other ATRT subgroups that express neural-like features. We identify five DNA methylation subgroups associated with anatomical sites and SMARCB1 mutation patterns. Groups 1, 3, and 4 exhibit cytotoxic T cell infiltration and expression of immune checkpoint regulators, consistent with a potential role for immunotherapy in rhabdoid tumor patients.

Bioinformatics (Oxford, England), 2019
Authors
Jackman, Shaun D, Mozgacheva, Tatyana, Chen, Susie, O'Huiginn, Brendan, Bailey, Lance, Birol, Inanc, Jones, Steven J M
Publication Abstract
The ORCA bioinformatics environment is a Docker image that contains hundreds of bioinformatics tools and their dependencies. The ORCA image and accompanying server infrastructure provide a comprehensive bioinformatics environment for education and research. The ORCA environment on a server is implemented using Docker containers, but without requiring users to interact directly with Docker, suitable for novices who may not yet have familiarity with managing containers. ORCA has been used successfully to provide a private bioinformatics environment to external collaborators at a large genome institute, for teaching an undergraduate class on bioinformatics targeted at biologists, and to provide a ready-to-go bioinformatics suite for a hackathon. Using ORCA eliminates time that would be spent debugging software installation issues, so that time may be better spent on education and research.

Bioinformatics (Oxford, England), 2019
Authors
Warren, René L, Coombe, Lauren, Mohamadi, Hamid, Zhang, Jessica, Jaquish, Barry, Isabel, Nathalie, Jones, Steven J M, Bousquet, Jean, Bohlmann, Joerg, Birol, Inanç
Publication Abstract
In the modern genomics era, genome sequence assemblies are routine practice. However, depending on the methodology, resulting drafts may contain considerable base errors. Although utilities exist for genome base polishing, they work best with high read coverage and do not scale well. We developed ntEdit, a Bloom filter-based genome sequence editing utility that scales to large mammalian and conifer genomes.

Cancers, 2019
Authors
Ho, Cally J, Gorski, Sharon M
Publication Abstract
Despite advances in diagnostic tools and therapeutic options, treatment resistance remains a challenge for many cancer patients. Recent studies have found evidence that autophagy, a cellular pathway that delivers cytoplasmic components to lysosomes for degradation and recycling, contributes to treatment resistance in different cancer types. A role for autophagy in resistance to chemotherapies and targeted therapies has been described based largely on associations with various signaling pathways, including MAPK and PI3K/AKT signaling. However, our current understanding of the molecular mechanisms underlying the role of autophagy in facilitating treatment resistance remains limited. Here we provide a comprehensive summary of the evidence linking autophagy to major signaling pathways in the context of treatment resistance and tumor progression, and then highlight recently emerged molecular mechanisms underlying autophagy and the p62/KEAP1/NRF2 and FOXO3A/PUMA axes in chemoresistance.

Nature communications, 2019
Authors
Sharma, Govinda, Rive, Craig M, Holt, Robert A
Publication Abstract
Cytotoxic CD8{{sup}}+{{/sup}} T cells recognize and eliminate infected or malignant cells that present peptide epitopes derived from intracellularly processed antigens on their surface. However, comprehensive profiling of specific major histocompatibility complex (MHC)-bound peptide epitopes that are naturally processed and capable of eliciting a functional T cell response has been challenging. Here, we report a method for deep and unbiased T cell epitope profiling, using in vitro co-culture of CD8{{sup}}+{{/sup}} T cells together with target cells transduced with high-complexity, epitope-encoding minigene libraries. Target cells that are subject to cytotoxic attack from T cells in co-culture are isolated prior to apoptosis by fluorescence-activated cell sorting, and characterized by sequencing the encoded minigenes. We then validate this highly parallelized method using known murine T cell receptor/peptide-MHC pairs and diverse minigene-encoded epitope libraries. Our data thus suggest that this epitope profiling method allows unambiguous and sensitive identification of naturally processed and MHC-presented peptide epitopes.

Blood, 2019
Authors
Hilton, Laura K, Tang, Jeffrey, Ben-Neriah, Susana, Alcaide, Miguel, Jiang, Aixiang, Grande, Bruno M, Rushton, Christopher K, Boyle, Merrill, Meissner, Barbara, Scott, David W, Morin, Ryan D
Publication Abstract
High-grade B-cell lymphomas with MYC and BCL2 and/or BCL6 rearrangements (HGBL-DH/THs) include a group of diffuse large B-cell lymphomas (DLBCLs) with inferior outcomes after standard chemoimmunotherapy. We recently described a gene expression signature that identifies 27% of germinal center B-cell DLBCLs (GCB-DLBCLs) as having a double-hit-like expression pattern (DHITsig) and inferior outcomes; however, only half of these cases have both MYC and BCL2 translocations identifiable using standard breakapart fluorescence in situ hybridization (FISH). Here, 20 DHITsig+ GCB-DLBCLs apparently lacking MYC and/or BCL2 rearrangements underwent whole-genome sequencing. This revealed 6 tumors with MYC or BCL2 rearrangements that were cryptic to breakapart FISH. Copy-number analysis identified 3 tumors with MYC and 6 tumors with MIR17HG gains or amplifications, both of which may contribute to dysregulation of MYC and its downstream pathways. Focal deletions of the PVT1 promoter were observed exclusively among DHITsig+ tumors lacking MYC translocations; this may also contribute to MYC overexpression. These results highlight that FISH fails to identify all HGBL-DH/THs, while revealing a range of other genetic mechanisms potentially underlying MYC dysregulation in DHITsig+ DLBCL, suggesting that gene expression profiling is more sensitive for identifying the biology underlying poor outcomes in GCB-DLBCL.

Proceedings of the National Academy of Sciences of the United States of America, 2019
Authors
Shen, Yaoqing, Grisdale, Cameron J, Islam, Sumaiya A, Bose, Pinaki, Lever, Jake, Zhao, Eric Y, Grinshtein, Natalie, Ma, Yussanne, Mungall, Andrew J, Moore, Richard A, Lun, Xueqing, Senger, Donna L, Robbins, Stephen M, Wang, Alice Yijun, MacIsaac, Julia L, Kobor, Michael S, Luchman, H Artee, Weiss, Samuel, Chan, Jennifer A, Blough, Michael D, Kaplan, David R, Cairncross, J Gregory, Marra, Marco A, Jones, Steven J M
Publication Abstract
Glioblastoma multiforme (GBM) is the most deadly brain tumor, and currently lacks effective treatment options. Brain tumor-initiating cells (BTICs) and orthotopic xenografts are widely used in investigating GBM biology and new therapies for this aggressive disease. However, the genomic characteristics and molecular resemblance of these models to GBM tumors remain undetermined. We used massively parallel sequencing technology to decode the genomes and transcriptomes of BTICs and xenografts and their matched tumors in order to delineate the potential impacts of the distinct growth environments. Using data generated from whole-genome sequencing of 201 samples and RNA sequencing of 118 samples, we show that BTICs and xenografts resemble their parental tumor at the genomic level but differ at the mRNA expression and epigenomic levels, likely due to the different growth environment for each sample type. These findings suggest that a comprehensive genomic understanding of in vitro and in vivo GBM model systems is crucial for interpreting data from drug screens, and can help control for biases introduced by cell-culture conditions and the microenvironment in mouse models. We also found that lack of expression in pretreated GBM is linked to hypermutation, which in turn contributes to increased genomic heterogeneity and requires new strategies for GBM treatment.

Cold Spring Harbor molecular case studies, 2019
Authors
Wong, Derek, Shen, Yaoqing, Levine, Adrian B, Pleasance, Erin, Jones, Martin, Mungall, Karen, Thiessen, Brian, Toyota, Brian, Laskin, Janessa, Jones, Steven J M, Marra, Marco A, Yip, Stephen
Publication Abstract
Effective management of brain and spine tumors relies on a multidisciplinary approach encompassing surgery, radiation, and systemic therapy. In the era of personalized oncology, the latter is complemented by various molecularly targeting agents. Precise identification of cellular targets for these drugs requires comprehensive profiling of the cancer genome coupled with an efficient analytic pipeline, leading to an informed decision on drug selection, prognosis, and confirmation of the original pathological diagnosis. Acquisition of optimal tumor tissue for such analysis is paramount and often presents logistical challenges in neurosurgery. Here, we describe the experience and results of the Personalized OncoGenomics (POG) program with a focus on tumors of the central nervous system (CNS). Patients with recurrent CNS tumors were consented and enrolled into the POG program prior to accrual of tumor and matched blood followed by whole-genome and transcriptome sequencing and processing through the POG bioinformatic pipeline. Sixteen patients were enrolled into POG. In each case, POG analyses identified genomic drivers including novel oncogenic fusions, aberrant pathways, and putative therapeutic targets. POG has highlighted that personalized oncology is truly a multidisciplinary field, one in which neurosurgeons must play a vital role if these programs are to succeed and benefit our patients.

Annual review of genomics and human genetics, 2019
Authors
Garrison, Nanibaa' A, Hudson, Māui, Ballantyne, Leah L, Garba, Ibrahim, Martinez, Andrew, Taualii, Maile, Arbour, Laura, Caron, Nadine R, Rainie, Stephanie Carroll
Publication Abstract
Indigenous scholars are leading initiatives to improve access to genetic and genomic research and health care based on their unique cultural contexts and within sovereign-based governance models created and accepted by their peoples. In the past, Indigenous peoples' engagement with genomicresearch was hampered by a lack of standardized guidelines and institutional partnerships, resulting in group harms. This article provides a comparative analysis of research guidelines from Canada, New Zealand, Australia, and the United States that pertain to Indigenous peoples. The goals of the analysis are to identify areas that need attention, support Indigenous-led governance, and promote the development of a model research policy framework for genomic research and health care that has international relevance for Indigenous peoples.

Clinical cancer research : an official journal of the American Association for Cancer Research, 2019
Authors
Jones, Martin R, Williamson, Laura M, Topham, James T, Lee, Michael K C, Goytain, Angela, Ho, Julie, Denroche, Robert E, Jang, GunHo, Pleasance, Erin, Shen, Yaoquing, Karasinska, Joanna M, McGhie, John P, Gill, Sharlene, Lim, Howard J, Moore, Malcolm J, Wong, Hui-Li, Ng, Tony, Yip, Stephen, Zhang, Wei, Sadeghi, Sara, Reisle, Carolyn, Mungall, Andrew J, Mungall, Karen L, Moore, Richard A, Ma, Yussanne, Knox, Jennifer J, Gallinger, Steven, Laskin, Janessa, Marra, Marco A, Schaeffer, David F, Jones, Steven J M, Renouf, Daniel J
Publication Abstract
Gene fusions involving neuregulin 1 () have been noted in multiple cancer types and have potential therapeutic implications. Although varying results have been reported in other cancer types, the efficacy of the HER-family kinase inhibitor afatinib in the treatment of fusion-positive pancreatic ductal adenocarcinoma is not fully understood.
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